But Maloney added: "Even for the game at the weekend, it's sort of day-to-day. We saw him last night with regards to the preparation for the game and then he wasn't in today.
"I'll speak to him this afternoon and then he'll make a call for tomorrow. And then I'd imagine he'll make the call for the game at the weekend.
"But, if it's this weekend, great. If it isn't, then we'll prepare for it with that one."
Maloney, who has managed Hibernian and Wigan, admitted it would be "strange" if he has to take charge at Rugby Park.
"We'll definitely miss him if he's not there but you also have to respect what's happened the last few days," he said.
"The impact that he's had over, what was it, since October, it's been nothing short of incredible really - the things that he does with the players and the staff.
"So we will miss him, but we'll be prepared. We've got some brilliant senior players, but we'll see. We'll let him make the call."
Maloney did not expect any new signings to be made, such as the reported bid for Oviedo's Egyptian winger Haissem Hassan, before Sunday's game and admitted those matters were still exclusively between O'Neill and chief executive Michael Nicholson.
The former Scotland midfielder knew there was interest in midfielder Arne Engels and right-back Alistair Johnston, but had no reason to believe they would not be in the squad to face Kilmarnock.